Efficient trapping of bacteria from whole blood is essential for point-of-care diagnostics of sepsis at an early stage in order to reduce morbidity and mortality. However, low bacteria concentration and the presence of blood cells hinder the trapping efficiency of bacteria from whole blood. As red blood cells comprise 94.9% of total blood cells, lysing the red blood cells using saponin could effectively attenuate the influence of the blood component on the bacteria-trapping process. In this situation, long-range bacteria trapping from whole blood using a hybrid electrokinetic based lab-on-a-chip device becomes promising. In this paper, through developing a multi-physical lattice Boltzmann method with Langevin dynamics, the continuous trapping process of S. aureus in a microfluidic channel with quadrupole electrodes under combined alternating-current electrothermal electrohydrodynamic force and negative dielectrophoresis force is numerically investigated and optimized at various parametric conditions. Based on the statistical data, a stable bacteria recovery rate of 68.4%–74.5% is successfully achieved with respect to different bacteria densities under appropriate operational conditions of the designed lab-on-a-chip device. The current work demonstrates the potential of continuous bacteria trapping from whole blood using hybrid electrokinetic phenomena.